Influenza virus characterisation, December 2019

Surveillance report
Publication series: Influenza Virus Characterisation
Time period covered: 2019–20 influenza season

European Centre for Disease Prevention and Control. Influenza virus characterisation, summary Europe,
December 2019. Stockholm: ECDC; 2020.

This is the third report for the 2019–20 influenza season.

Executive summary

As of week 1/2020, 42 844 influenza detections had been reported across the WHO European Region; 85% type A viruses, with A(H3N2) prevailing over A(H1N1)pdm09, and 15% type B viruses, with 531 (92%) of 576 ascribed to a B/Victoria lineage.

Since the November 2019 characterisation report1, 12 shipments of influenza-positive specimens from EU/EEA countries have been received at the London WHO CC, the Francis Crick Worldwide Influenza Centre (WIC). A total of 397 virus specimens have been received, with collection dates after 31 August 2019, and these will be considered at the February 2020 WHO influenza vaccine recommendation meeting.

Seventeen A(H1N1)pdm09 test viruses from EU/EEA countries have been characterised antigenically since the last report, with 16 showing good reactivity with antiserum raised against the 2019–20 vaccine virus, A/Brisbane/02/2018. The 21 test viruses with collection dates from week 40/2019 genetically characterised at the WIC have fallen within subclades of clade 6B.1A: 15 6B.1A5A, 3 6B.1A5B, 1 6B.1A6 and 2 6B.1A7.

Since the last report, 17 A(H3N2) viruses have been characterised antigenically. Of the 17, 12 were clade 3C.3a viruses that were antigenically similar to the vaccine virus, A/Kansas/14/2017. The remaining five were subgroup 3C.2a1b+T135K viruses that were poorly recognised by the vaccine virus. In total, 57 viruses have been characterised genetically at the WIC: 38 clade 3C.3a, 11 3C.2a1b+T131K, three 3C.2a1b+T135K-A and five 3C.2a1b+T135K-B.

Fourteen B/Victoria-lineage viruses have been characterised in this reporting period, all of which gave antigenic profiles characteristic of subgroup 1A(Δ3)B viruses, represented by B/Washington/02/2019, the vaccine virus for the 2020 southern hemisphere season, with the subgroup having been confirmed for nine of the viruses. In total, all of 29 viruses characterised genetically at the WIC have been subgroup 1A(Δ3)B.

The single B/Yamagata-lineage virus characterised antigenically in this reporting period reacted poorly with antiserum raised against the vaccine virus B/Phuket/3073/2013 (clade 3) and only reacted well with an antiserum raised against a B/Yamagata-lineage virus carrying multiple unusual substitutions in HA1. While all recently circulating B/Yamagata-lineage viruses belong to genetic clade 3 and contain at least two HA amino acid substitutions compared to B/Phuket/3073/2013 (HA1 L172Q and M251V), antigenic effects have been minimal based on earlier reports. Genetic characterisation of B/Yamagata-lineage viruses received is pending.